AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252290
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0181	83	hypothetical protein
#1	TM0653	72	conserved hypothetical protein
#2	TM0655	24	conserved hypothetical protein
#3	TM0656	281	conserved hypothetical protein
#4	TM0703	42	competence-damage inducible protein, putative
#5	TM0770	60	conserved hypothetical protein
#6	TM0826	127	hypothetical protein
#7	TM0828	29	sugar kinase, pfkB family
#8	TM0839	54	rod shape-determining protein RodA
#9	TM0840	39	hypothetical protein
#10	TM0842	37	response regulator
#11	TM0883	135	conserved hypothetical protein
#12	TM1095	300	adenylosuccinate lyase
#13	TM1530	101	electron transfer flavoprotein, beta subunit
#14	TM1537	57	Mg-protoporphyrin IX monomethyl ester oxidative cyclase-related protein
#15	TM1597	49	hypothetical protein
#16	TM1598	32	RNA polymerase sigma-E factor
#17	TM1864	71	hypothetical protein

Motif 1
TGGATAGTGAGGAGGTGAAAAT         	0	1	0
AATCACCATGAGAGGTGATTGT         	0	71	1
   AAATTTCAGAGGGGAGGGATTAAC    	2	7	1
ATGGAAATAGGGAGGTGCAGGGT        	3	2	0
AATTAGAAGGCGAGGTGAGATC         	5	1	0
AAATCAGAACTGAGGTGAAAGG         	5	48	1
AATCTATCCTGGAGGTGATTGG         	6	1	0
GAATCAAAAACGAGGTGATGCCTC       	6	113	1
CTTTTGACTTCGAGGTGATCGT         	7	17	1
AGTGATAAAGGGAGGAGTTCGCA        	10	24	1
TTTTATCACGGGAGGTGGAGAGA        	11	2	0
CAAATGTTTCAGAGGTGTGTAAGAAATATTT	11	84	1
TCTCAAATGTGGAGGTGATACTT        	11	122	1
CCCTCGAGGACGAGGAGAAAGATCAGACTCA	12	31	0
TCCTCGTCCTCGAGGGGTTCGAATATTTGAA	12	46	1
TTTGACCTTTGGAGGAGATATCTGAGGAGGC	13	73	1
AGATATCTGAGGAGGCGAAGAGC        	13	88	1
GAATACCCACAGAGGTGATTCTC        	14	44	1
ATAGTTACGTGGAGGTGATCACAAGTT    	15	6	0
AGTCTTAATACGAGGAGGAAACGGTT     	16	16	1
ACGGGGGTCTGGAGGAGATTGTT        	17	58	1
          ********* *
MAP Score: 43.7973

Motif 2
CAATTTCAAAGTGTTATTATTTGGATAGTG	0	23	0
TTCTCAAAGCGTGTTAAAATCACCATGAGA	0	54	1
TTTTTCCTTTCTGGTATAATCTAATTAGTC	1	30	1
TTATAATTATGTGGTAAAATAAATCCAGGA	3	39	0
AACGATGAGGCTGTTCTAATTGAATCGAGA	3	97	1
GAAAGGGGGGTGGGTATAATAATGTCTGTG	3	212	1
ATCCCCCTGTGTGTTATCATATCACTGAGG	4	13	1
TTATCATTGGTTGTTATAATTAGAAGGCGA	5	19	0
ATAACAACCAATGATAAAATCAGAACTGAG	5	32	1
AACGTCTCCAGGGTTAAAATCTATCCTGGA	6	19	0
TACATTCTCCGGGTTTTAATTGTAATGATC	6	53	1
TAAAGGTTTGGGGTTAGAATCAAAAACGAG	6	97	1
       TCGATGTTAAAATTAGTGATAAA	10	3	1
TCCACCTCCCGTGATAAAATTTTCTGATGT	11	14	1
CGTCCTCGAGGGGTTCGAATATTTGAAAGG	12	50	1
GTTGCTGCAGCTGTTCTCATGTTCGTGGGA	13	43	1
CCTTCTTTCTGTGTTAGAATACCCACAGAG	14	28	1
TTTTTCGGCTGTGATAAAATAAATTCAGCC	17	14	1
          **********
MAP Score: 18.6952

Motif 3
CAATTTCAAAGTGTTATTATTTGGATAGTGAGGAGGTGA	0	14	0
TAATAACACTTTGAAATTGTTTCTCAAAGCGTGTTAAAA	0	34	1
TTTTTCCTTTCTGGTATAATCTAATTAGTCTGAGCAAAC	1	30	1
CACCTCCCTATTTCCATGGTATTTCCTGGATTTATTTTA	3	16	1
TAATTATAAACTGTAATGATTTTGAATAGTTACATTAAA	3	60	1
AACGATGAGGCTGTTCTAATTGAATCGAGAAAAGATTGC	3	97	1
ATCCCCCTGTGTGTTATCATATCACTGAGGAGGGATCGT	4	13	1
AAACCTTTAATTGGACTTGTATGGATCATTACAATTAAA	6	67	0
GTCTATTCGTTTGTTCTCGTGTGGTATGGTCCCACC   	8	7	0
ACCTCCACATTTGAGATGGTGTAAAATATTTCTTACACA	11	99	0
TCTCAAATCGCTTTTCTGGTTTCTCGTTGCGATGGCGTT	12	173	1
CCAACGGCTTCTTATCTTGTTTTTCCTGTTGTTGCGCTC	12	237	1
TTTCCTGTTGTTGCGCTCGTGTTCACGAGAGATCTGTTT	12	258	1
GTTGCTGCAGCTGTTCTCATGTTCGTGGGATTTGACCTT	13	43	1
TCCAGACCCCCGTGTCTGGTATCCTGAGGCTGAATTTAT	17	32	0
          ***  ** ** *     **
MAP Score: 6.59891

Motif 4
TTTCCGGTTGCTGCAGCTGTTCTCATGTTCGTGG	13	37	1
AGAATACCCACAGAGGTGATTCTC          	14	43	1
TCACATGAAACAGGGTCTTTTCTC          	12	0	0
AGCCCCGCTTCGGCGGGGTTTTTCCTTTCTGGTA	1	12	1
CAATCACCTCCAGGATAGATTTTAACCCTGGAGA	6	11	1
TATCCTGAGGCTGAATTTATTTTATCACAGCCGA	17	18	0
ATGGTATTTCCTGGATTTATTTTACCACATAATT	3	31	1
TACGATCGAGCCGAGTTGTTTCTGGTGCTGTCCT	12	87	1
GATTTTAACCCTGGAGACGTTTTATTACATTCTC	6	28	1
TAATTATAAACTGTAATGATTTTGAATAGTTACA	3	60	1
AAAAGCAGATCGCAATCTTTTCTCGATTCAATTA	3	113	0
ACATTAAACGATGAGGCTGTTCTAATTGAATCGA	3	91	1
AAGAGGACATCAGAAAATTTTATCACGGGAGGTG	11	16	0
GATCACCTCCACGTAACTATTCTACTATAAAGTG	15	17	1
   AACATCCCCCTGTGTGTTATCATATCACTGA	4	7	1
          * * ** * *****
MAP Score: 5.03774

Motif 5
TTGAGAAACAATTTCAAAGTGTTATTATTTGGA	0	28	0
  ACAATCACCTCTCATGGTGATTTTAACACGC	0	62	0
TTACATTAAACGATGAGGCTGTTCTAATTGAAT	3	89	1
TTGAATCGAGAAAAGATTGCGATCTGCTTTTAG	3	116	1
GTGGGTATAATAATGTCTGTGATACTGAACAAG	3	221	1
   AACATCCCCCTGTGTGTTATCATATCACTG	4	7	1
CTGATTTTATCATTGGTTGTTATAATTAGAAGG	5	22	0
TTAAAATCTATCCTGGAGGTGATTGG       	6	3	0
GTTAGAATCAAAAACGAGGTGATGCCTC     	6	109	1
CTCACTTTTGACTTCGAGGTGATCGT       	7	13	1
ACCATCTCAAATGTGGAGGTGATACTT      	11	118	1
ACCCTGTTTCATGTGAGTCTGATCTTTCTCCTC	12	18	1
TTTCTCCTCGTCCTCGAGGGGTTCGAATATTTG	12	42	1
GGACAGATTACGATCGAGCCGAGTTGTTTCTGG	12	79	1
TTCTTTGCGAAACTGGTGGCGATCAGAGGAAAG	12	122	0
CTTTTCTGGTTTCTCGTTGCGATGGCGTTGTGG	12	183	1
TTCACGAGAGATCTGTTTGGGAGGGAAAAAG  	12	279	1
   ATGAAAGCACTGAAGCTGATAATCGAGTTT	13	7	1
GGGATTTGACCTTTGGAGGAGATATCTGAGGAG	13	69	1
GAGGAGATATCTGAGGAGGCGAAGAGC      	13	84	1
GGCTTCGGCCCCTTCTTTCTGTGTTAGAATACC	14	18	1
TAGAATAGTTACGTGGAGGTGATCACAAGTT  	15	8	0
          *  *** ******
MAP Score: 2.33258

Motif 6
TTATTTGGATAGTGAGGAGGTGAAAAT     	0	5	0
AAAATCACCATGAGAGGTGATTGT        	0	69	1
     AAATTTCAGAGGGGAGGGATTAAC   	2	5	1
ATACCATGGAAATAGGGAGGTGCAGGGT    	3	6	0
CTTGACAACGAAAGGGGGGTGGGTATAATAAT	3	203	1
ACTATAGTGGACAAAGGGGTTGGGAACTTT  	3	261	1
ATATGATAACACACAGGGGGATGTT       	4	3	0
TTATCATATCACTGAGGAGGGATCGT      	4	26	1
TTGTTATAATTAGAAGGCGAGGTGAGATC   	5	7	0
TAAAATCAGAACTGAGGTGAAAGG        	5	46	1
GGTTAGAATCAAAAACGAGGTGATGCCTC   	6	108	1
CCTCGAAGTCAAAAGTGAGGAG          	7	0	0
ATTCGTTTGTTCTCGTGTGGTATGGTCCCACC	8	10	0
AAATTAGTGATAAAGGGAGGAGTTCGCA    	10	19	1
GAAAATTTTATCACGGGAGGTGGAGAGA    	11	6	0
GTCAAATGTTTCAGAGGTGTGTAAGAAATATT	11	82	1
CTGGTGGCGATCAGAGGAAAGAAGGACAGCAC	12	111	0
GGAGGAGATATCTGAGGAGGCGAAGAGC    	13	83	1
         AAAAAAGGGGCTTCGGCCCCTTC	14	1	1
CTAACACAGAAAGAAGGGGCCGAAGCCCCTTT	14	13	0
TAGAATACCCACAGAGGTGATTCTC       	14	42	1
ACTATTCTACTATAAAGTGAGGTGTTG     	15	32	1
          ******* ** *
MAP Score: 1.12389